@mjangelvortex
The issue with AJ and FS is that they are the “straight men” in the jokes normally, so they can get a few lines, but they are difficult to include as key characters in a short scene. Their characters and humor work after a build-up (eg Honest Apple, Filly Vanilli)
PP is easy for fourth-wall breaking and quick humor. Rarity may be Flanderized, but that also makes for quick humor. RD is “action girl” so that makes her easy to include. And of course the movie had to be centered around Twilight, but she’s also easy to include in one-scene jokes if needed.
@mjangelvortex
True. I heard that Rarity and Capper actually had a mini-romance side-story that was cut for time, and I imagine a swashbuckling section with RD might’ve been cut short as well. But yeah, AJ and Shy were really shafted. But then again, the other new characters didn’t have a huge impact either (aside from Tempest, everyone loves her).
@Crowley
Yeah, it’s a shame. I can understand why they had to do it though. Juggling 7 main characters from the TV series, introducing said main characters to a new and general audience, and introducing a whole bunch of different new characters in the movie was probably a bit more than what they could handle here. They probably bit more what they could chew.
At least Rarity and Rainbow Dash got a little bit of attention too since they both had little side plots with Capper and the Parrot Pirates. Likewise Spike managed to be helpful multiple times during the story. Applejack and Fluttershy were pretty much the two that got the short end of the stick here.